Magnesium in PDB 3f61: Crystal Structure of M. Tuberculosis Pknb LEU33ASP/VAL222ASP Double Mutant in Complex with Adp
Enzymatic activity of Crystal Structure of M. Tuberculosis Pknb LEU33ASP/VAL222ASP Double Mutant in Complex with Adp
All present enzymatic activity of Crystal Structure of M. Tuberculosis Pknb LEU33ASP/VAL222ASP Double Mutant in Complex with Adp:
2.7.11.1;
Protein crystallography data
The structure of Crystal Structure of M. Tuberculosis Pknb LEU33ASP/VAL222ASP Double Mutant in Complex with Adp, PDB code: 3f61
was solved by
C.A.Mieczkowski,
T.Alber,
Tb Structural Genomics Consortium (Tbsgc),
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
37.77 /
1.80
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
38.981,
51.542,
152.434,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
20.3 /
22.8
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Crystal Structure of M. Tuberculosis Pknb LEU33ASP/VAL222ASP Double Mutant in Complex with Adp
(pdb code 3f61). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the
Crystal Structure of M. Tuberculosis Pknb LEU33ASP/VAL222ASP Double Mutant in Complex with Adp, PDB code: 3f61:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 3f61
Go back to
Magnesium Binding Sites List in 3f61
Magnesium binding site 1 out
of 4 in the Crystal Structure of M. Tuberculosis Pknb LEU33ASP/VAL222ASP Double Mutant in Complex with Adp
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Crystal Structure of M. Tuberculosis Pknb LEU33ASP/VAL222ASP Double Mutant in Complex with Adp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg310
b:21.1
occ:1.00
|
O2A
|
A:ADP340
|
2.0
|
20.4
|
1.0
|
OD2
|
A:ASP156
|
2.0
|
22.5
|
1.0
|
O
|
A:HOH411
|
2.1
|
19.9
|
1.0
|
OD1
|
A:ASN143
|
2.1
|
17.5
|
1.0
|
O1B
|
A:ADP340
|
2.1
|
25.9
|
1.0
|
O
|
A:HOH410
|
2.2
|
24.1
|
1.0
|
CG
|
A:ASP156
|
3.2
|
22.1
|
1.0
|
PA
|
A:ADP340
|
3.2
|
21.0
|
1.0
|
PB
|
A:ADP340
|
3.2
|
27.4
|
1.0
|
CG
|
A:ASN143
|
3.2
|
17.8
|
1.0
|
O3B
|
A:ADP340
|
3.6
|
28.6
|
1.0
|
O3A
|
A:ADP340
|
3.6
|
21.1
|
1.0
|
O5'
|
A:ADP340
|
3.8
|
19.7
|
1.0
|
ND2
|
A:ASN143
|
3.8
|
17.7
|
1.0
|
CB
|
A:ASP156
|
3.9
|
19.5
|
1.0
|
NZ
|
A:LYS40
|
4.0
|
24.7
|
1.0
|
O
|
A:HOH315
|
4.2
|
27.9
|
1.0
|
O
|
A:HOH397
|
4.2
|
27.0
|
1.0
|
OD1
|
A:ASP156
|
4.2
|
29.0
|
1.0
|
O
|
A:ALA142
|
4.3
|
18.6
|
1.0
|
CB
|
A:ASN143
|
4.5
|
17.3
|
1.0
|
O1A
|
A:ADP340
|
4.5
|
22.6
|
1.0
|
CG
|
A:MET155
|
4.6
|
19.5
|
1.0
|
O2B
|
A:ADP340
|
4.6
|
29.9
|
1.0
|
CA
|
A:ASN143
|
4.6
|
17.1
|
1.0
|
C
|
A:ALA142
|
4.8
|
17.7
|
1.0
|
CE
|
A:LYS140
|
4.8
|
18.3
|
1.0
|
N
|
A:ASN143
|
4.9
|
16.9
|
1.0
|
SD
|
A:MET155
|
5.0
|
27.8
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 3f61
Go back to
Magnesium Binding Sites List in 3f61
Magnesium binding site 2 out
of 4 in the Crystal Structure of M. Tuberculosis Pknb LEU33ASP/VAL222ASP Double Mutant in Complex with Adp
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Crystal Structure of M. Tuberculosis Pknb LEU33ASP/VAL222ASP Double Mutant in Complex with Adp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg311
b:25.8
occ:1.00
|
O
|
A:HOH385
|
2.9
|
30.6
|
1.0
|
O
|
A:HOH404
|
3.0
|
31.9
|
1.0
|
N
|
A:ALA142
|
3.1
|
18.4
|
1.0
|
CD
|
A:PRO141
|
3.5
|
17.7
|
1.0
|
CB
|
A:ALA142
|
3.5
|
17.6
|
1.0
|
CD
|
A:ARG101
|
3.7
|
34.4
|
1.0
|
N
|
A:PRO141
|
3.7
|
17.5
|
1.0
|
CG
|
A:LYS140
|
3.8
|
16.2
|
1.0
|
CB
|
A:LYS140
|
3.9
|
17.6
|
1.0
|
CA
|
A:ALA142
|
3.9
|
17.1
|
1.0
|
CB
|
A:PRO141
|
4.0
|
17.0
|
1.0
|
CD
|
A:LYS140
|
4.0
|
18.3
|
1.0
|
C
|
A:PRO141
|
4.0
|
17.8
|
1.0
|
CA
|
A:PRO141
|
4.1
|
18.3
|
1.0
|
CG
|
A:PRO141
|
4.2
|
19.1
|
1.0
|
CE2
|
A:TYR182
|
4.2
|
21.4
|
1.0
|
C
|
A:LYS140
|
4.3
|
17.5
|
1.0
|
NE
|
A:ARG101
|
4.3
|
39.3
|
1.0
|
CE
|
A:LYS140
|
4.4
|
18.3
|
1.0
|
CB
|
A:ARG101
|
4.4
|
24.1
|
1.0
|
CG
|
A:ARG101
|
4.4
|
28.6
|
1.0
|
CZ
|
A:TYR182
|
4.7
|
20.7
|
1.0
|
CA
|
A:LYS140
|
4.7
|
17.1
|
1.0
|
OH
|
A:TYR182
|
4.8
|
22.3
|
1.0
|
CD2
|
A:TYR182
|
4.8
|
21.0
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 3f61
Go back to
Magnesium Binding Sites List in 3f61
Magnesium binding site 3 out
of 4 in the Crystal Structure of M. Tuberculosis Pknb LEU33ASP/VAL222ASP Double Mutant in Complex with Adp
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Crystal Structure of M. Tuberculosis Pknb LEU33ASP/VAL222ASP Double Mutant in Complex with Adp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg312
b:31.3
occ:1.00
|
O
|
A:HOH394
|
2.7
|
39.6
|
1.0
|
O1A
|
A:ADP340
|
2.7
|
22.6
|
1.0
|
N
|
A:SER23
|
3.0
|
19.4
|
1.0
|
N
|
A:MET22
|
3.1
|
19.5
|
1.0
|
CA
|
A:GLY20
|
3.1
|
17.9
|
1.0
|
C
|
A:GLY20
|
3.2
|
17.7
|
1.0
|
N
|
A:GLY21
|
3.2
|
18.9
|
1.0
|
O3A
|
A:ADP340
|
3.4
|
21.1
|
1.0
|
O
|
A:HOH412
|
3.4
|
31.2
|
1.0
|
N
|
A:GLY20
|
3.5
|
17.8
|
1.0
|
CB
|
A:SER23
|
3.6
|
19.4
|
1.0
|
PA
|
A:ADP340
|
3.6
|
21.0
|
1.0
|
CA
|
A:SER23
|
3.8
|
18.5
|
1.0
|
CA
|
A:MET22
|
3.8
|
19.4
|
1.0
|
C
|
A:MET22
|
3.8
|
19.2
|
1.0
|
OG
|
A:SER23
|
3.8
|
21.6
|
1.0
|
O
|
A:SER23
|
3.9
|
20.0
|
1.0
|
O
|
A:GLY20
|
3.9
|
18.0
|
1.0
|
CB
|
A:MET22
|
4.1
|
19.9
|
1.0
|
C
|
A:GLY21
|
4.1
|
20.0
|
1.0
|
CA
|
A:GLY21
|
4.2
|
19.1
|
1.0
|
O3B
|
A:ADP340
|
4.2
|
28.6
|
1.0
|
O
|
A:HOH358
|
4.3
|
26.2
|
1.0
|
C
|
A:SER23
|
4.3
|
19.4
|
1.0
|
O
|
A:HOH479
|
4.3
|
42.0
|
1.0
|
PB
|
A:ADP340
|
4.5
|
27.4
|
1.0
|
C
|
A:PHE19
|
4.7
|
17.5
|
1.0
|
O2A
|
A:ADP340
|
4.7
|
20.4
|
1.0
|
O5'
|
A:ADP340
|
4.8
|
19.7
|
1.0
|
C5'
|
A:ADP340
|
4.8
|
19.1
|
1.0
|
O2B
|
A:ADP340
|
5.0
|
29.9
|
1.0
|
O
|
A:MET22
|
5.0
|
18.9
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 3f61
Go back to
Magnesium Binding Sites List in 3f61
Magnesium binding site 4 out
of 4 in the Crystal Structure of M. Tuberculosis Pknb LEU33ASP/VAL222ASP Double Mutant in Complex with Adp
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Crystal Structure of M. Tuberculosis Pknb LEU33ASP/VAL222ASP Double Mutant in Complex with Adp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg313
b:53.5
occ:1.00
|
CB
|
A:ASN127
|
3.5
|
26.1
|
1.0
|
O
|
A:HOH450
|
3.5
|
40.3
|
1.0
|
CA
|
A:ALA267
|
3.6
|
21.8
|
1.0
|
CG
|
A:ASN127
|
3.7
|
30.4
|
1.0
|
CD
|
A:ARG270
|
3.8
|
26.1
|
1.0
|
CB
|
A:ALA267
|
3.8
|
22.4
|
1.0
|
CA
|
A:GLN124
|
4.0
|
22.5
|
1.0
|
O
|
A:CYS123
|
4.0
|
19.8
|
1.0
|
OD1
|
A:ASN127
|
4.0
|
36.9
|
1.0
|
O
|
A:HOH452
|
4.1
|
34.5
|
1.0
|
N
|
A:ALA267
|
4.1
|
21.1
|
1.0
|
CG
|
A:GLN124
|
4.1
|
27.6
|
1.0
|
N
|
A:GLN124
|
4.3
|
21.4
|
1.0
|
C
|
A:CYS123
|
4.3
|
20.4
|
1.0
|
CB
|
A:ARG270
|
4.3
|
21.1
|
1.0
|
ND2
|
A:ASN127
|
4.3
|
29.2
|
1.0
|
CB
|
A:GLN124
|
4.6
|
23.5
|
1.0
|
O
|
A:ALA266
|
4.6
|
20.0
|
1.0
|
C
|
A:ALA266
|
4.6
|
21.4
|
1.0
|
O
|
A:HOH374
|
4.7
|
30.0
|
1.0
|
CG
|
A:ARG270
|
4.7
|
23.0
|
1.0
|
C
|
A:ALA267
|
4.7
|
21.9
|
1.0
|
CB
|
A:CYS123
|
4.8
|
19.3
|
1.0
|
O
|
A:ALA267
|
4.8
|
21.6
|
1.0
|
NE
|
A:ARG270
|
4.9
|
28.7
|
1.0
|
CA
|
A:ASN127
|
5.0
|
25.3
|
1.0
|
|
Reference:
C.Mieczkowski,
A.T.Iavarone,
T.Alber.
Auto-Activation Mechanism of the Mycobacterium Tuberculosis Pknb Receptor Ser/Thr Kinase. Embo J. V. 27 3186 2008.
ISSN: ISSN 0261-4189
PubMed: 19008858
DOI: 10.1038/EMBOJ.2008.236
Page generated: Wed Aug 14 13:33:59 2024
|